General Information

Concerns surrounding a new strain of SARS-CoV-2, the virus behind the COVID-19 pandemic, have been developing. B.1.1.7, also known as Variant of Concern 202012/01 (VOC 202012/01) or 20B/501Y.V1, was first identified in the UK in early December 2020 and has since been detected in the US and other countries. The growing concern is primarily because it has shown to be significantly more transmissible than other variants. The data presented was gratefully sourced from GISAID.

As of 01/19/2021, there's been 18074 sequences detected in over 41 countries under this strain (see table for definition).
In the US, there's been 86 sequences detected in over 15 states.

Table 1.1: Key Mutations that define the strain
Gene	Nucleotide Mutations	Amino Acid Changes
ORF1ab	C3266T, T6953C, C5387A, 11288:11296 deletion	T1001I, I2230T, A1708D
S	A23062T, C23270A, A23402G, C23603A, C23708T, T24505G, G24913C	DEL69-70, DEL144Y, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
N	GAT28279CTA, C28976T	D3L, S235F
ORF8	G28047T, C27971T, A28110G	R52I, Q27_, Y73C

Figure 1.1: genetic distance (root-to-tip), a measure of evolutionary changes, plotted for strain and non-strain (related) samples (excluding other well known VOCs e.g. B.1.135).

State Prevalence

Figure 2.1: spatial (geographical) prevalence of the B117 strain across California.

Figure 2.2: temporal (over time) prevalence of the strain across California.

National Prevalence

Figure 3.1: the spatial (geographical) prevalence of the strain across the US.

Figure 3.2: the temporal (over time) prevalence of the strain across the US.

Global Prevalence

More detailed information on global prevalence of SARS-CoV-2 strains of concern can be found in this post.

Figure: the spatial (geographical) prevalence of the strain across the world.

Figure 4.2: the temporal (over time) prevalence of the strain across the world.

Notes on Sampling

As figure 3.2 indicates, the majority of B.1.1.7 genomes identified in the US (so far), were identified by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Since it was not an unbiased approach, it does not indicate the true prevalence of the B117 lineage in the US. This only tells us that the lineage is present in the US.
P.S: estimates of true prevalence in the US are discussed in this post

Figure 5: a simple illustration of how genomic surveillance of COVID-19 samples could allow us to elucidate an increasingly clear picture of how the virus is evolving and spreading. The pictures above are electromagnetic microscopy images of SARS-CoV-2 (credit: NIAID) that are "crappified" (salt & pepper noise) to varying degrees depending on the rate of COVID-19 sequencing at each location. As a reference, we include a clear picture on the right to indicate that a 5% genomic sampling rate would be an ideal (first) objective to be able to observe statistically significant phenomena. across the world.

Comments

Research laboratories across the US are encouraged to contribute to COVID-19 genomic sequencing efforts. More detailed information can be found here.

Specifically when uploading genomes to GISAID or GenBank, please indicate if the sample was identified via S-gene target failures (SGTF). This can be indicated under the fields "purpose_of_sequencing" (GISAID) or "Additional host information". This will help in identifying the true prevalence of the lineage across the country.

via GIPHY